Dereplication of a FASTA file

Purpose

This tool takes a FASTA-formatted sequence file and removes
all clones (100% sequence identity clones). It returns a ZIP
file that contains the dereplicated sequences, a names file
for running Mothur on dereplicated sequences, and a file with
two columns. The first column will have the representative
sequence tag, whereas the second column will have the
"multiplicity" of that sequence, namely, the number of
clones of that sequence (including that sequence). For an example:

S11235 1
S81321 2
S34558 17
S91442 1
S33377 34
...

For instance, if your FASTA file contains all unique sequences,
then the second column will contain only 1s.
You can use this file to create a UniFrac environment file.